Any mods that fix the problem of merging ships with the merge button and no attachment points popping up.

[Cashdesigner]

What the title says.

[Geonovast]

You don't need a mod to fix this, you need the re-root tool.

Once you've done the merge (or grabbed a subassembly), you can use the re-root tool when it's shadowed red.  Once you set the root to a part with an open node, you'll have an attachment point.

The re-root tool is up next to the rotate tool.  It's the Z shape with a box on each end.